Diversity characterization and association analysis of agronomic traits in a Chinese peanut (Arachis hypogaeaL.) mini‐core collection

Abstract

Association mapping is a powerful approach for exploring the molecular basis of phenotypic variations in plants. A peanut (Arachis hypogaea L.) mini-core collection in China comprising 298 accessions was genotyped using 109 simple sequence repeat (SSR) markers, which identified 554 SSR alleles and phenotyped for 15 agronomic traits in three different environments, exhibiting abundant genetic and phenotypic diversity within the panel. A model-based structure analysis assigned all accessions to three groups. Most of the accessions had the relative kinship of less than 0.05, indicating that there were no or weak relationships between accessions of the mini-core collection. For 15 agronomic traits in the peanut panel, generally the Q + K model exhibited the best performance to eliminate the false associated positives compared to the Q model and the general linear model-simple model. In total, 89 SSR alleles were identified to be associated with 15 agronomic traits of three environments by the Q + K model-based association analysis. Of these, eight alleles were repeatedly detected in two or three environments, and 15 alleles were commonly detected to be associated with multiple agronomic traits. Simple sequence repeat allelic effects confirmed significant differences between different genotypes of these repeatedly detected markers. Our results demonstrate the great potential of integrating the association analysis and marker-assisted breeding by utilizing the peanut mini-core collection.

Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability

“…Indeed, four of the accessions screened in this study were chosen from the United States peanut minicore collection. Previous minicore screens have also shown that there is huge variability for traits such as water use efficiency (Singh et al 2014), oil content (Wang et al 2011a,b), bacterial wilt disease (Jiang et al 2014), resistance to abiotic and biotic stresses (Upadhyaya et al 2013), and agronomic traits (Pandey et al 2014). Sufficient variation has been identified among tetraploid accessions through transcriptome sequencing for performing QTL analysis with high density marker linkage maps.…”

“…Evaluation has demonstrated significant phenotypic diversity for numerous traits, including resistance to leaf spots, tomato spotted wilt virus, other biotic stresses, for tolerance to drought or heat stress, and for early maturity (Isleib et al 1995; Anderson et al 1996; Upadhyaya 2003, 2005, Upadhyaya et al 2006a,b; Selvaraj et al 2011; Wang et al 2011a; Jiang et al 2014; Pandey et al 2014; Singh et al 2014). To date, these have not been accompanied by molecular characterization at SNP levels.…”

Development of SSR markers and identification of major quantitative trait loci controlling shelling percentage in cultivated peanut (Arachis hypogaea L.)

“…Jiang et al (2014) reported five, two and two significant associated alleles for shelling percentage in three field trials, respectively, through association analysis in Chinese peanut mini-core collection of 298 accessions. Only one SSR allele, 9B4-260, was associated with shelling percentage in all three trials (1.49–2.98% PVE) (Jiang et al 2014). No major QTLs were reported to be consistently expressed so far.…”

Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.)

“…Cultivated peanut is an allotetraploid (AABB, 2n = 4x = 40) crop formed through the natural hybridization of its two progenitor diploids, A. duranensis (AA, 2n = 2x = 20) and A. ipaensis (BB, 2n = 2x = 20)1415. Positive correlations were revealed between plant height and yield-related traits, such as pod length, pod width, hundred pod weight, seed length, seed width and hundred seed weight16 in Chinese peanut mini-core collection. Majority of the cultivated peanuts in China and many other countries belong to erect/bunch type, and the long height of peanut crop could lead to lodging.…”